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Sars International Centre for Marine Molecular Biology

Former Groups of Sars Centre

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2006 - 2014  Jiang Group,  Ascidian Notochord Morphogenesis

(May 2006 - Dec 2014)

Development of the notochord
Cell & Developmental Biology / Ciona
 

We are interested in how differentiated cells are organized into complex tissues and organs, and how this process evolves. The ascidian notochord provides an elegant system for studying this process. In contrast to the vertebrate notochord, which consists of thousands of still dividing cells whose positions and movements during development are difficult to trace, ascidian notochord has only 40 cells, which are post-mitotic at the beginning of morphogenesis. During a process called convergent extension, a four by ten sheet of differentiated notochord cells are organized into a single column of 40-stacked cells. Following convergent extension, notochord development continues as individual cells elongate and produce extracellular matrix along the anterior/posterior axis. Finally, these extracellular lumens fuse to form a tube that runs the length of the larval tail. Ascidian notochord at the swimming larval stage functions as a hydrostatic “skeleton” essential for the locomotion of the tadpoles.

In addition to this simple and stereotypic mode of development and morphogenesis in notochord, ascidian offers several other advantages for developmental genetic and cell biology studies. First, ascidians belong to proto-chordates that have diverged from vertebrate lineage before whole genome duplications; therefore they reveal a minimal gene repertoire for building a chordate. Second, genomes of both Ciona intestinalis and Ciona savignyi, two commonly used species in the laboratory, have been sequenced, providing a platform for genomic and genetic studies. Third, electroporation provides an efficient method for routine gene manipulation and generation of transgenic animals. Fourth, large scale culture of Ciona and their being self-fertilizing hermaphrodites makes ascidians attractive animal models for classic genetic study. Finally, fast and external embryonic development and transparent embryos allows sub-cellular level imaging and experimental manipulation of specific cell biology processes.

We have used molecular markers and confocal imaging to describe tubulogenesis in the developing Cionanotochord. During tubulogenesis each notochord cell establishes de novo apical domains, and undergoes a mesenchymal epithelial transition to become an unusual epithelial cell with two opposing apical domains. Concomitantly, extracellular luminal matrix is produced and deposited between notochord cells (Fig. 1 and Fig. 2). Subsequently, each notochord cell simultaneously executes two types of crawling movements bidirectionally along the anterior/posterior axis on the inner surface of notochordal sheath. Lamellipodia-like protrusions results in cell lengthening along the anterior/posterior axis, while the retraction of trailing edges of the same cell leads to the merging of the two apical domains (Fig. 3). As a result, the notochord cells acquire endothelial-like shape and forms the wall of the central lumen. Inhibition of actin polymerization prevents the cell movement and tube formation.  Ciona notochord tube formation utilizes an assortment of common and fundamental cellular processes including cell shape change, apical membrane biogenesis, cell/cell adhesion remodeling, dynamic cell crawling, and lumen matrix secretion.

Our group now uses Ciona notochord tubulogenesis as experimental model to address the molecular mechanisms of tube formation. We perform functionally analyses of various cell biology processes and aim to provide mechanistic insights as how each contributes to, and how their actions are coordinated during, the construction of the tube. Specific questions and projects include:

  1. Polarity establishment; interaction between apical/basal polarity and planar cell polarity pathways, and functional significance of cell polarities in organizing cell shape changes, cell movement, and metabolic activities of notochord cells during tube formation.
  2. Secretory pathways (nature of secretory vesicles and their directional trafficking) for extracellular matrix production and apical/luminal membrane biogenesis.
  3. Molecular mechanisms for dynamic remodeling of cell adhesion complexes, including adherens junctions and tight junctions, during the rearrangement of notochord cells (Fig. 4) as they form a tube
  4. Molecular and mechanistic basis of the force generation underlying cell shape changes and cell movements 

 

Di Jiang
 

Postdoc, National Institute of Health andUniversity of California Santa Barbara 1999-2006
PhD, The George Washington University, USA, 1999

Postdoctoral Fellows

  • 2006-2009 Satoko Awazu
  • 2008-2014 Elsa Denker
  • 2007-2010 Bo Dong
  • 2010-2014 Ivonne Sehring

PhD Students

  • 2008-2012 Wei Deng

Department Engineer

  • 2009-2012 Mary Laplante
  • 2008-2014 Birthe Mathiesen     Facility Tech/Dept Engineer

Research Technician

  • 2011-2012 Punit Bhattachan     Research Assistant
  • 2007-2009 Erika Broberg

Guest Students and Researchers

  • 2007 Jamie Kugler         PhD Student,     Weill Cornell Medical College
  • 2014 May-July Julien Audisso      Master Student,     University of Paris VII
  • 2007 Jun-Aug Agnes Miermont    Master Student,     University of Paris VII

2007 - 2014  Adamska Group,  Developmental Signalling in Marine Sponges

(Aug 2007 - Dec 2014)

Sponge development

Signalling and Genome studies / calcareous sponges
 

During animal development, formation of morphologically complex structures from the fertilized egg requires precise cell to cell communication. Surprisingly, only a handful of intercellular signalling pathways are used throughout the animal kingdom: wnt, tgf-ß, hedgehog, receptor tyrosine kinase and notch. To gain insight into evolutionary origin of these important pathways, and establish simple models in which to study embryonic development, it is crucial to include basal animals in the suite of model species. Recent work on Nematostella vectensis and other cnidarians demonstrated that the invention of the major signalling pathways predated divergence of cnidarians and bilaterians. It also indicates that to gain insight into the ancestral state of the developmental signalling, it is necessary to look into animals representing earlier branching clades.
Sponges are considered to be the sister group of “true” animals, the eumetazoa, and thus provide the ultimate outgroup for all comparative studies of animal development. Recently, the genome of Amphimedon queenslandica, a Great Barrier Reef demosponge has been sequenced at the DOE Joint Genome Institute.
Analysis of the Amphimedon genome and expression studies throughout embryonic development demonstrate that all major metazoan signalling pathways are used during sponge embryogenesis. Wnt, tgf-ß, and hedgeling a related to hedgehog transmembrane protein  genes are expressed in dynamic, partially overlapping patterns in Amphimedon embryos.
Similarly to higher animals, the wnt pathway appears to be used in establishment of the anterior-posterior axis of the sponge embryo. These results open way to further research that would provide insights into developmental mechanisms of all multicellular animals from both molecular biology and evolutionary perspective.

Maja Adamska

2005-2007 Postdoc, University of Queensland, Australia 
2001-2004 Postdoc, University of Michigan, USA 
2001 Doctorate, University of Halle-Wittenberg Halle, Germany

Postdoctoral Fellows

  • 2008 - 2013 Svein Leininger
  • 2009 Friederike Hoffmann

PhD Students

  • Sofia V. Fortunato     PhD student, Sept 2012 - May 2014, Postdoc, June - Dec 2014

Department Engineer

  • 2012 - 2014 Mary Laplante    
  • 2011 - 2013 Corina Guder    
  • 2010 - 2011 Signe Jordal    
  • 2008 - 2010 Christin Zwafink    

Research Technician

  • 2011 - 2014 Jing Liu    
  • 2009 - 2011 Brith Bergum    
  • 2007 - 2009 Erika Broberg    

Guest Researchers

  • 2014 May Ilya E. Borisenko, St. Petersburg State University (Master Student: Feb - March)
  • 2014 Feb - May Anthony Leon, ENS de Lyon (Master Student)
  • 2014 Feb - April Ina J. Andresen, University of Oslo (Master Student)
  • 2013 June - Aug Katarzyna Sluzek, LMU Munich (Master Student)
  • 2012 Aug - Sept Oliver Voigt, LMU Munich (Postdoc)

2006 - 2011  Lenhard Group,  Bioinformatics of Transcription and Transcriptional Gene Regulation

(2006 - 2011)

Mechanisms of gene regulation

Post-genome Bioinformatics
 

This group had a joint appointment between Bergen Centre for Computational Science (BCCS) and Sars Centre, both units of Uni Research AS.

Transcriptional regulation has been identified as the top-priority research subject of advanced post-genome bioinformatics. Binding site specificities of individual eukaryotic transcription factors are notoriously low, which precludes their application to genome-wide analysis. The only available biologically meaningful transcription factor binding site data comes from relatively rare experimental analysis of inferred regulatory regions. Some progress was made upon observation that some tissue-specific genes are regulated by cis-regulatory modules (CRM), i.e. clusters of binding sites for tissue-specific regulatory elements. Another major leap was facilitated by cross-species comparisons of regulatory sequences (phylogenetic footprinting). This step has been successfully combined with other detection methods such as CRM detection, resulting in significant increase in the specificity of predictions.

We are working on several new approaches to harness the new discoveries and newly available data into a next-generation gene regulation bioinformatics platform. We assembled JASPAR, the world´s first open access database of transcription factor binding site profiles from higher eukaryotes. In addition e developed a computational framework for transcription factor binding site analysis (TFBS) and applied it to quantitatively demonstrate the ability of cross-species comparisons to drastically improve detection rate of transcription factor binding sites. ConSite is our web-based application for the phylogenetic footprinting enhanced detection of transcription factor binding sites.

Based on conceptual framework inherited from studies in bacteria and yeast, previous methods primarily focused on regions 5' upstream from the inferred transcription binding sites. New incoming data is starting to invalidate this as a general approach: many genes are regulated by non-coding elements distributed along the length of the entire gene. Our analysis of the genomic context and organization of 3583 ultra-conserved non-coding regions (UCRs) in the human genome, revealed that they tend to cluster near and around genes involved in fundamental developmental processes in vertebrates, and most often have known homologs in invertebrates (e.g. in Drosophila). The genomic organization of SCR clusters revealed a striking array of long-range enhancers around key genes, sometimes spanning areas of more than 1 MB. This discovery provides an argument against focusing on proximal promoter regions in search for key regulatory elements, and implies the existence of long-range, chromatin-level regulatory mechanisms. We continue to explore the long range regulatory elements across higher eukaryotes.

Another exciting area of research research we are involved in is the analysis of mammalian transcriptome. In collaboration with RIKEN Genome Science Center (Japan), we are dissecting the loci with demonstrated complex transcription patterns, including the occurences of natural antisense, bidirectional promoters and cis-regulatory chains.

Future projects and goals:

  • Elucidation of the genomic organization long range regulatory elements in metazoan genomes and inference of their physiological function hrom hints provided by their sequence, genomic organization and evolution
  • Building predictive models for regulatory determinants of context-specific gene expression that include long-range regulatory elements
  • Bioinformatics of vertebrate development - transcriptional regulatory network approach to vertebrate embryonic development circuitry
  • Exploring the structure and establishment of classification scheme for vertebrate core promoters and transcription start sites
  • Development of methods for predicting the effects of regulatory variation in the genome

Boris Lenhard

 

2006-2011 Associate Group Leader, Sars Centre
2005-present Group leader/Senior scientist,Bergen Center for Computational Science,
2002-2005 Group Leader/Assistant Professor, Karolinska Institutet,  
2000-2002 Postdoctoral Researcher, Karolinska Institutet, Sweden,  
1999 PhD, University of Zagreb, Croatia,  

New Contact Information

Imperial College London, MRC Clinical Sciences Centre
Computational Regulatory Genomics
b.lenhard@imperial.ac.uk 

Postdoctoral Fellows

  • 2005 - 2009 David Fredman
  • 2008 - present Christopher Previti (BFS)September

PhD Students

  • Altuna Akalin
  • Xianjun Dong
  • Pär Engström
  • Ying Sheng
  • Chirag Nepal

1999 - 2008  Becker Group,  Vertebrate Genome Regulation using Zebrafish

(Jan 1999 - Dec 2008)

Vertebrate development

Genetic screens for regulatory elements / zebrafish

 

Zebrafish have a generation time of only three months and are bred in the laboratory in large numbers, making them suitable for transgene- based genomic analysis. Embryonic development from a fertilized egg to a swimming fish with a functional visual system takes only five days, and development of the entire body can be studied in great detail in the living animal using transgenic fish where gene expression is visible under the microscope. As the zebrafish genome nears completion it becomes evident that this small vertebrate has a developmental gene repertory that is near identical to that of humans. The way the genome shapes a vertebrate embryo is studied in zebrafish in forward genetic screens that aim either at recovering mutations that cause specific defects during embryonic development as well as through examining gene expression. Mutations that affect the activity of crucial genes can also give important clues about human heritable diseases. For instance all major vertebrate organs are found in the young fish and their development can be observed. Our own interest is the development of the embryonic forebrain, specifically the retina, but we have recently started to work on many more organs, based on the finding that developmental regulatory genes affect many different structures. For example the fish below shows expression of GFP under the control of regulatory elements of the inhibitor of differentiation 1 gene (id1), which is expressed in the bones, skin, retina, pineal, optic tectum, and cerebellum.
All teleosts genomes have undergone an additional duplication and as a result a number of genes are found in duplicate in the zebrafish genome when compared to tetrapods. The duplicated genes share the function of the ancestral single gene. An example is shown below, where the two loci of the pax6.1 and pax6.2 genes are seen to have complementary expression patterns in the retina, diencephalon, hindbrain and spinal cord, where the mammalian single gene is highly expressed. We have found that, as postulated by the duplication, degeneration, complementation (DDC) model, this subfunctionalization is based upon the loss of specific regulatory elements from one or the other locus when compared to the human chromosomal locus.
Our laboratory uses the zebrafish to characterize vertebrate transcriptional regulation at the genome level. In an enhancer detection screen where we generated and screened around 15000 retroviral insertions in the zebrafish germ line, we kept and characterized about 350 transgenic lines with yellow fluorescent protein (YFP) expression in the central or peripheral nervous system and mapped the insertions to the zebrafish genome sequence.
Surprisingly, a number of gene expression patterns were found more than once, and upon mapping we discovered that they demarcate the same large chromosomal segments of several hundred kb around developmental regulatory genes, suggesting that these genes are regulated by long-range regulatory elements that are situated at a long distance from the coding sequence. In other cases we found that, while the insertion was near or even inside a gene, the expression pattern was that of a gene further away, which in every case were also regulatory genes (encoding transcription factors, growth factors or micro RNAs, to name a few).
Some of these chromosomal segments that are now termed genomic regulatory blocks were also independently discovered through bioinformatic methods by way of association of large numbers of highly conserved non coding elements (HCNEs) around regulatory genes (see Lenhard lab web site). Since then, many of these HCNEs have been shown to act as positive regulatory elements, or enhancers, and they are indeed found not only close to the gene, but far up- or downstream of the gene they regulate, as well as in introns of neighboring genes, in some cases (in the human genome) a Mb or more away. Our main projects at present are the characterization and annotation of entire genomic regulatory blocks for their regulatory content, especially those that have likely connection to human genetic diseases.

Thomas Becker

PhD Columbia University, 1994

University of Sydney, Brain and Mind Research Institute
100 Mallett St.Camperdown NSW 2050 Australia
tbecker@med.usyd.edu.au 

Postdoctoral Fellows

  • 2006 - 2008 Øyvind Drivenes    
  • 2008 - 2008 Anna Zofia Komisarczuk    
  • 2008 - 2008 Beena Punnamoottil    
  • 2006 - 2008 Silke Rinkwitz    

PhD Students

  • Pavla Navratilova
  • Puja Gupta

Department Engineer

  • Mary A. Laplante

Research Technicians - Zebrafish Facility

  • Sîan Phillips
  • Øyvind Reinshol
  • Eilen Myrvold

2004 - 2008  Technau Group,  Molecular Developmental Genetics of Cnidaria

(Aug 2004 - Dec 2008)

Cnidarian development

Evolution of Development /Nematostella

 

Cnidaria are the best studied outgroup to the Bilateria. Our group established the new model systemNematostella vectensis, a brackish water sea anemone, to study different aspects of the evolution of developmental processes.

Nematostella belongs to the class Anthozoa. Molecular and morphological studies suggest that Anthozoa is the basal group among the Cnidaria. Nematostella is easy to culture in the lab and gametogenesis can be induced. Thus, embryonic development is easily accessible.For comparison, we also work on the hydrozoan Hydra, a fresh water polyp, one of the best studied cnidarians. 

Our research is focused on four areas:

The evolution of the third germ layer, the mesoderm. In order to trace the evolution of the mesoderm, we study the role of “mesodermal” genes in a diploblast animal, i.e. that consists of two germ layers only, ectoderm and endoderm. We recently isolated a number of “mesodermal” genes and studied their expression pattern in detail throughout early embryonic and larval development until metamorphosis into a primary polyp. We focus on transcription factors that are crucially involved in the formation and differentiation of the mesoderm in Bilateria, such as Brachyury, snail, twist, forkhead and gata factors. To understand how these genes are regulated, we investigate the role of the major signaling pathways, in particular the FGF/ras/MAPK pathway and the TGF-ß pathway. Since the formation of the mesoderm is closely linked to gastrulation in all Bilateria, we examine the cellular and molecular processes during gastrulation and metamorphosis. 
One of the major derivatives of the mesoderm is muscle tissue. Nematostella, like all other anthozoans, have strong retractor muscles that differentiate on one side of the endodermal mesenteries. By PCR and by an extensive EST screen we identified a number of muscle specific genes that we use as marker genes to follow the differentiation of the musculature in polyps. We currently examine how the differentiation of muscle tissue in Nematostella is regulated.

The molecular network of Brachyury. The T-box gene brachyury plays a crucial role in mesoderm differentiation of vertebrates. In the diploblast Hydra and Nematostella, brachyury is expressed in the blastopore and its derivative in the polyp, the hypostome, which is equivalent to the Spemann organizer. Comparative expression studies in a number of basal Bilateria showed that many aspects such as the early blastoporal expression and its derivatives, are conserved among the animal kingdom. It is, however, unclear to what extent the molecular network of brachyury is also conserved. Identified upstream and downstream components of Brachyury in chordates suggest that Brachyury mediates between patterning and morphogenesis. We are therefore interested in the identification of downstream and upstream genes of brachyury as well as interacting proteins in cnidarians.

Comparative and functional genomics. We carried out an extensive EST screen from a cDNA library of mixed embryonic and larval stages from Nematostella. Currently, in a collaboration with the Joint Genome Institute (USA), the genome of Nematostella is being sequenced and a draft genome is expected for the end of 2004. The Nematostella genome represents the first genome from a diploblast animal and will undoubtedly provide interesting insights into the evolution of metazoan genomes, complexity and diversification of basal metazoans. By the comparison of the Nematostella genome and EST data with those of Bilateria, we envisage to infer the genetic repetoire of the Ur-Eumetazoa, the common ancestor of Cnidaria and Bilateria.

Evolution of the nervous system. Cnidaria were the first animals in evolution with a nervous system. Most species only have a diffuse nerve net, which however, undergoe constant turnover and renewal from differentiating stem cells. We are interested in the molecular network of the differentiation of the nervous system and its derivatives such as eyes.

Ulrich Technau 

PhD University of Frankfurt, 1996

New Contact Information 

Univ.-Prof. Dr. Ulrich Technau
Dept. for Molecular Evolution and DevelopmentCentre for Organismal Systems Biology
Faculty of Life Sciences, University of Vienna
Althanstrasse 14
1090 Wien
Austria
Tel. +43-(1) 4277-56740
Mobile: +43-664-6027756740
email

Postdoctoral Fellows

  • 2005 - 2008 Grigory Genikhovich    
  • 2005 - 2007 Fabian Rentzsch    
  • 2007 - 2008 Patrick Steinmetz    

PhD Students

  • 2004 - 2007 Holger Bielen    
  • 2004 - 2007 Jens Fritzenwanker    
  • 2004 - 2008 Michael Saina    

Department Engineer

  • 2005 - 2007 Eduard Renfer    

Research Technician

  • 2005 - 2007 Monica Martinussen    

1999 - 2004  Olsen Group,  Germline Development

(Jan 1999 - Oct 2004)

Germline development

Developmental biology /zebrafish

Segregation of germ soma occurs early during animal development. In several species, both vertebrates and invertebrates, subcellular structures called germ granules (or nuage) which consist of RNA and proteins, have been found to segregate with the germ cell lineage. Based on the correlation between germ granule distribution and the development of the germ cell lineage, these granules are thought to function in regulation and/or maintainance of the germ cell fate. 

Several genes controlling germ cell formation in the fruit fly Drosophila melanogaster and the nematode C. elegans have been identified and found to encode germ plasm or germ granule components. The function of the germ granules and its components is still unknown.

Our goal is to gain insight into the molecular mechanisms regulating germ cell fate in vertebrates. We are using zebrafish (Danio rerio) as our model organism. 

To this end, we have isolated zebrafish vlg, a homologue of Drosophila vasa, a gene which is expressed in the germline. Vasa is a DEAD box RNA helicase and the protein most likely functions as a translational regulator. The Vasa protein has been shown to be a germ granule component in flies, nematodes and chicken. Possible targets for Vasa protein may be the RNA components of the germ granules or granule interacting mRNAs. In order to gain insight into the function(s) of zebrafish Vlg protein during germline development, we have decided to search for its potential RNA targets.

Lisbeth C. Olsen

PhD University of Bergen Norway, 1992

Lisbeth.Olsen@uib.no

PhD Students

  • 2001 - 2005 Anne Vatland Krøvel    
  • 1999 - 2003 Karin Wibrand    

Research Assistants

  • 2004 - 2004 Sara Ferreira    
  • 1999 - 2001 Anne Vatland Krøvel    

Department Engineers

  • 1999 - 2004 Lill K.Knudsen (50%)    

Masters Students

  • 2003 - 2004 Janniche Torsvik    
  • 2001 - 2003 Marianne Hauglid    
  • 1999 - 2000 Hege Holsvik    

1998 - 2003  Cunningham Group,  Comparable Immunology

(Sept 1998 - Sept 2003)

Vertebrate immune system

Comparative Immunology / fish and agnathans

 

Evidence obtained from a wide variety of species suggests that immunoglobulins, T cell receptors and major histocompatibility complex (MHC) molecules are present in all vertebrates including bony fish and elasmobranchs (sharks and rays). In contrast, these molecules appear to be absent from agnathans (a sister group to vertebrates) and invertebrates. Similarly, it is likely that while vertebrates possess a wide variety of immune cell types and a complex molecular signalling network of cytokines and receptors to coordinate and control immune responses, the degree of complexity in invertebrates is likely to be less pronounced. The major aim of the comparative immunology group is to understand how the complex vertebrate immune system evolved from its invertebrate counterpart. To this end we are studying groups of MHC related genes which have co-evolved and individual genes which have are either been proven to exist, or are thought to exist in higher invertebrates and agnathans.

Vertebrate genomes contain regions which are paralogous to the MHC. Paralogous genes within the same species are descended from the same ancestral gene by duplication and divergence during evolution. It has been proposed that the MHC arose as a result of ancient chromosomal duplications that took place in a common ancestor of the vertebrates. We are studying the nature of these paralogs in agnathan hagfish to determine how the vertebrate paralogs evolved and to determine if a primitive MHC gene exists within the invertebrate paralogs. Individual genes being studied in agnathans include those encoding (1) transcription factors involved in the differentiation of immune cell repertoires; (2) the SWAP-70 gene, which has been shown in vertebrates to play a central role in immunoglobulin class switching and (3) the genes encoding TGFb and interleukin 1 family members. Knowledge derived from these studies will not only inform us about the nature and complexity of the agnathan immune system, it will also provide information which will help us to understand the evolution of vertebrate immunity.

Charles Cunningham 

PhD University of Aberdeen, 1985

Scientists

  • 1998 - 2003 Pauline M. Cupit    

Postdoctoral Fellows

  • 1999 - 2002 Sumati Subramaniam    
  • 1998 - 1999 Gregory White    

Research Assistants

  • 2002 - 2003 Anette Hansen    
  • 2002 - 2003 Erling Høivik    
  • 2002 Ranjan Chrisanthar    
  • 2000 Christine Gjerdrum    

Department Engineers

  • 2002 - 2003 Vibeke H. Oland (50%)    
  • 2002 Åse-Lill Helgesen (50%)    
  • 2001 - 2002 Elin Danielsen (50%)    
  •  Litta Olsen    

Master Student

  • 2000 - 2002 Marianne Bjørdal